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At least 127 records · Page 7

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Lim, Kap↗

A Study of the X(sup 2) Sigma(sup +) and A(sup 2) Pi States of MgAr(sup +) and MgKr(sup +)

The ground (sup 2)Sigma(sup +) and lowest excited (sup 2)Pi states of MgAr(sup +) and MgKr(sup +) are studied using the singles and doubles configuration interaction (SDCI) approach, in conjunction with large basis sets. The effect of Mg core correlation and core polarization are accounted for using the core-polarization potential (CPP) approach. Franck-Condon factors, oscillator strengths, radiative lifetimes, dissociation energies, bond lengths, and excitation energies are reported. The computed results are in good agreement with the available experimental data.

Bauschlicher, Charles W., Jr.↗

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) (Muster T et al., 1993, J Virol 67:6642-6647) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class (Ji X, Zhang P, Armstrong RN, Gilliland GL, 1992, Biochemistry 31:10169-10184) was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(3)2(1)2, with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Schistosoma japonicum/enzymology/genetics/immunolo↗

Formal Modeling of Multi-Agent Systems using the Pi-Calculus and Epistemic Logic

Multi-agent systems have become important recently in computer science, especially in artificial intelligence (AI). We allow a broad sense of agent, but require at least that an agent has some measure of autonomy and interacts with other agents via some kind of agent communication language. We are concerned in this paper with formal modeling of multi-agent systems, with emphasis on communication. We propose for this purpose to use the pi-calculus, an extension of the process algebra CCS. Although the literature on the pi-calculus refers to agents, the term is used there in the sense of a process in general. It is our contention, however, that viewing agents in the AI sense as agents in the pi-calculus sense affords significant formal insight. One formalism that has been applied to agents in the AI sense is epistemic logic, the logic of knowledge. The success of epistemic logic in computer science in general has come in large part from its ability to handle concepts of knowledge that apply to groups. We maintain that the pi-calculus affords a natural yet rigorous means by which groups that are significant to epistemic logic may be identified, encapsulated, structured into hierarchies, and restructured in a principled way. This paper is organized as follows: Section 2 introduces the pi-calculus; Section 3 takes a scenario from the classical paper on agent-oriented programming [Sh93] and translates it into a very simple subset of the n-calculus; Section 4 then shows how more sophisticated features of the pi-calculus may bc brought into play; Section 5 discusses how the pi-calculus may be used to define groups for epistemic logic; and Section 6 is the conclusion.

Rorie, Toinette↗

Cloud Structure Anomalies Over the Tropical Pacific During the 1997/98 El Nino

Satellite measurements of both cloud vertical structure and cloud-radiative forcing have been used to show that during the strong 1997/98 El Nino there was a substantial change in cloud vertical structure over the tropical Pacific Ocean. Relative to normal years, cloud altitudes were lower in the western portion of the Pacific and higher in the eastern portion. The reason for these redistributions was a collapse of the Walker circulation and enhanced large-scale upward motion over the eastern Pacific, both caused by the lack of a zonal sea surface temperature gradient during El Nino. It is proposed that these cloud structure changes, which significantly impact satellite measurements of the tropical Pacific's radiation budget, would serve as one useful means of testing cloud-climate interactions in climate models.

Cess, Robert D.↗

Measurements of $\pi ^\pm $, $K^\pm $, p and $\bar{p}$ spectra in $^{40}\hbox {Ar+}^{45}\hbox {Sc}$ collisions at 13A to 150A $\text{ Ge }\hspace{-1.00006pt}\text{ V }\!/\!c$

The NA61/SHINE experiment at the CERN Super Proton Synchrotron studies the onset of deconfinement in strongly interacting matter through a beam energy scan of particle production in collisions of nuclei of varied sizes. This paper presents results on inclusive double-differential spectra, transverse momentum and rapidity distributions and mean multiplicities of $\pi ^\pm $, $K^\pm $, p and $\bar{p}$ produced in $^{40}\hbox {Ar+}^{45}\hbox {Sc}$ collisions at beam momenta of 13A, 19A, 30A, 40A, 75A and 150A $\text{ Ge }\hspace{-1.00006pt}\text{ V }\!/\!c$. The analysis uses the 10% most central collisions, where the observed forward energy defines centrality. The energy dependence of the $K^\pm $/$\pi ^\pm $ ratios as well as of inverse slope parameters of the $K^\pm $ transverse mass distributions are placed in between those found in inelastic $p+p$ and central Pb + Pb collisions. The results obtained here establish a system-size dependence of hadron production properties that so far cannot be explained either within statistical or dynamical models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Theoretical electronic transition moments for the Ballik-Ramsay, Fox-Herzberg, and Swan systems of C2

Electronic transition moments and their variation with internuclear separation are calculated for the Ballik-Ramsay (b 3 Sigma g - a 3 Pi u), Fox-Herzberg (e 3 Pi g-a 3 Pi u) and Swan (d 3 Pi g-a 3 Pi u) band systems of C2, which appear in a variety of terrestrial and astrophysical sources. Electronic wave functions of the a 3 Pi u, b 2 Sigma g -, d 3 Pi g and e 3 Pi g states of C2 are obtained by means of a self-consistent field plus configuration interaction calculation using an atomic basis of 46 Slater-type orbitals, and theoretical potential energy curves and spectroscopic constants for the four electronic states were computed. The results obtained for both the potential energy curves and electronic transition moments are found to be in good agreement with experimental data.

Cooper, D. M.↗

Absolute Definition of Phase Shift in the Elastic Scattering of a Particle from Compound Systems

The projection of the target wave function on the total wave function of a scattered particle interacting with the target system is used to define an absolute phase shift including any multiples of pi. With this definition of the absolute phase shift, one can prove rigorously in the limit of zero energy for s-wave electrons scattered from atomic hydrogen that the triplet phase shift must approach a nonzero multiple of pi. One can further show that at least one pi of this phase shift is not connected with the existence of a bound state of the H- ion.

Temkin, A.↗

$K^{*}(892)^0$ meson production in inelastic p+p interactions at 40 and 80 $\text{ GeV }\!/\!c$ beam momenta measured by NA61/SHINE at the CERN SPS

Measurements of $K^{*}(892)^0$ resonance production via its $K^{+}\pi ^{-}$ decay mode in inelastic p+p collisions at beam momenta 40 and 80 $\text{ GeV }\!/\!c$ ($\sqrt{s_{NN}}=8.8$ and 12.3 $\text{ GeV }$) are presented. The data were recorded by the NA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. The template method was used to extract the $K^{*}(892)^0$ signal. Transverse momentum and rapidity spectra were obtained. The mean multiplicities of $K^{*}(892)^0$ mesons were found to be $(35.1 \pm 1.3 \mathrm {(stat)} \pm 3.6 \mathrm {(sys))} \cdot 10^{-3}$ at 40 $\text{ GeV }\!/\!c$ and $(58.3 \pm 1.9 \mathrm {(stat)} \pm 4.9 \mathrm {(sys))} \cdot 10^{-3}$ at 80 $\text{ GeV }\!/\!c$. The NA61/SHINE results are compared with the Epos1.99 and Hadron Resonance Gas models as well as with world data. The transverse mass spectra of $K^{*}(892)^0$ mesons and other particles previously reported by NA61/SHINE were fitted within the Blast-Wave model. The transverse flow velocities are close to 0.1–0.2 of the speed of light and are significantly smaller than the ones determined in heavy nucleus-nucleus interactions at the same beam momenta.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

On the length of the drift region in the Ramsey cavity

The interaction of atoms in a beam with the microwave field in a separated field geometry such as a Ramsey cavity is generally described in terms of the three regions traversed successively by the atoms, namely two interaction regions of length (l) separated by a drift, or free precession, region of length L. For a monokinetic beam of velocity v, the linewidth of the central fringe in the Ramsey resonance pattern is usually expressed as delta omega equals pi v/L. A more detailed calculation shows, however, that the linewidth is equal to pi v/L asterisk, where the equivalent drift L asterisk is larger than L by an amount of the order of l/L. The correction depends on the field distribution in the interaction regions. Its origin lies in the fact that atomic precession is not limited to the field-free regions but also occurs in the interaction regions, where atomic coherence builds up or decreases continuously. Although the correction to the equivalent length of the drift region is small, it may be relevant to the evaluation of the second-order Doppler effect bias in primary cesium-beam standards to the extent that the atomic velocity is deduced from the lineshape and from the geometrical parameters of the cavity. It is shown that in current and projected standards with atoms of average thermal velocity, use of corrected dimensions may lead to a change of the calculated bias of the order of 10(exp -14), which is significant at the levels of accuracy considered nowadays.

Thomann, Pierre↗

Unified Models of Turbulence and Nonlinear Wave Evolution in the Extended Solar Corona and Solar Wind

The PI (Cranmer) and Co-I (A. van Ballegooijen) made significant progress toward the goal of building a "unified model" of the dominant physical processes responsible for the acceleration of the solar wind. The approach outlined in the original proposal comprised two complementary pieces: (1) to further investigate individual physical processes under realistic coronal and solar wind conditions, and (2) to extract the dominant physical effects from simulations and apply them to a one-dimensional and time-independent model of plasma heating and acceleration. The accomplishments in the report period are thus divided into these two categories: 1a. Focused Study of Kinetic MHD Turbulence. We have developed a model of magnetohydrodynamic (MHD) turbulence in the extended solar corona that contains the effects of collisionless dissipation and anisotropic particle heating. A turbulent cascade is one possible way of generating small-scale fluctuations (easy to dissipate/heat) from a pre-existing population of low-frequency Alfven waves (difficult to dissipate/heat). We modeled the cascade as a combination of advection and diffusion in wavenumber space. The dominant spectral transfer occurs in the direction perpendicular to the background magnetic field. As expected from earlier models, this leads to a highly anisotropic fluctuation spectrum with a rapidly decaying tail in the parallel wavenumber direction. The wave power that decays to high enough frequencies to become ion cyclotron resonant depends on the relative strengths of advection and diffusion in the cascade. For the most realistic values of these parameters, though, there is insufficient power to heat protons and heavy ions. The dominant oblique waves undergo Landau damping, which implies strong parallel electron heating. We thus investigated the nonlinear evolution of the electron velocity distributions (VDFs) into parallel beams and discrete phase-space holes (similar to those seen in the terrestrial magnetosphere) which are an alternate means of heating protons via stochastic interactions similar to particle-particle collisions. 1b. Focused Study of the Multi-Mode Detailed Balance Formalism. The PI began to explore the feasibility of using the "weak turbulence," or detailed-balance theory of Tsytovich, Melrose, and others to encompass the relevant physics of the solar wind. This study did not go far, however, because if the "strong" MHD turbulence discussed above is a dominant player in the wind's acceleration region, this formalism is inherently not applicable to the corona. We will continue to study the various published approaches to the weak turbulence formalism, especially with an eye on ways to parameterize nonlinear wave reflection rates. 2. Building the Unified Model Code Architecture. We have begun developing the computational model of a time-steady open flux tube in the extended corona. The model will be "unified" in the sense that it will include (simultaneously for the first time) as many of the various proposed physical processes as possible, all on equal footing. To retain this generality, we have formulated the problem in two interconnected parts: a completely kinetic model for the particles, using the Monte Carlo approach, and a finite-difference approach for the self-consistent fluctuation spectra. The two codes are run sequentially and iteratively until complete consistency is achieved. The current version of the Monte Carlo code incorporates gravity, the zero-current electric field, magnetic mirroring, and collisions. The fluctuation code incorporates WKJ3 wave action conservation and the cascade/dissipation processes discussed above. The codes are being run for various test problems with known solutions. Planned additions to the codes include prescriptions for nonlinear wave steepening, kinetic velocity-space diffusion, and multi-mode coupling (including reflection and refraction).

Cranmer, Steven R.↗

Anisotropic Coarse-Grained Model for Conjugated Polymers: Investigations into Solution Morphologies

The optoelectronic properties of conjugated polymers are dictated by the interplay of multiscale structural features, including intrachain dihedrals, interchain pi-pi stacking, and the complex mesoscale morphology. While much is known about the structures of polymers with isotropically interacting monomers, little is known about polymers with strongly anisotropic backbone monomers, a class of materials to which conjugated polymers belong. Fundamental understanding is further complicated when the semiflexible and molecularly heterogeneous nature of conjugated polymers is taken into account. We present an anisotropic coarse-grained (CG) model for conjugated polymers that incorporates key molecular features (monomer anisotropy, intermonomer dihedrals, and side chains). Finally, the model is employed to characterize the single-chain conformational properties of conjugated polymers, revealing a rich temperature-dependent conformational landscape. These studies provide a critical link between CG molecular descriptors and conformational ordering in conjugated polymers.

36 MATERIALS SCIENCE↗

The Lunar Regolith as a Remote Sensing Target for the Lunar Reconnaissance Orbiter (LRO)

Of the 6 instruments and one technology demonstration aboard the LRO, only CRaTER does not measure some kind of interaction of particles with the lunar regolith. LEND detects neutron fluence that contains information about the number density of protons in the upper regolith. To infer the presence of protons, the PI must assume a model that characterizes the surface as a collection of atoms. Thus, LEND does not sense the regolith as a structure. LROC, LOLA, and LAMP sense reflected photons whose wavelength is much shorter than the median particle size in the regolith. The photons interact with electrons, either in atomic shells or in chemical bonds. These interactions occur within a nanometer or so of the surface of a particle. Thus, the particles are macroscopic objects and models of the reflection process invoke ray-tracing optics. DIVINER senses photons that have been emitted by surface particles through thermal phonon processes. The wavelengths detected by the instrument are of the same order as the median particle size, and the photons contain information on particle dimensions as well as the molecular bonds in the constituent compounds. The Mini-RF synthetic aperture radar generates and detects photons of a few centimeters wavelength that interact with the regolith as a dielectric, the dielectric properties of the particulate component being described through effective medium theory. However, the interaction with rocks (macroscopic objects of interest to geologists) can be characterized using Fresnel or Mie models of electromagnetic properties.

Mendell, Wendell W.↗

Amplitude Analysis of $\omega\pi^0$ Photoproduction at GlueX

Excited meson states can often lie hidden within mass spectra beneath more dominant resonances, making it difficult to extract their physical properties. We can unveil these states through amplitude analysis, which disentangles the overlapping states via fits to their unique production and decay angular distributions. Understanding the light-meson spectrum is essential for confirming Lattice QCD predictions, especially in regards to the search for possible hybrid mesons. The Gluonic Excitation (GlueX) experiment at Jefferson Lab aids this search by studying the production of excited light mesons in $\gamma p$ interactions in the 8.2 - 8.8 GeV photon-beam energy range. We show in these proceedings preliminary results of an amplitude analysis of a large $\omega\pi^0$ dataset, concentrating on measuring the interference between the $b_1(1235)$ and an excited $J^{PC}=1^{--}$ vector resonance.

Scheuer, Kevin↗

Seismic Waveform Inversion Capability on Resource-Constrained Edge Devices

Seismic full wave inversion (FWI) is a widely used non-linear seismic imaging method used to reconstruct subsurface velocity images, however it is time consuming, has high computational cost and depend heavily on human interaction. Recently, deep learning has accelerated it’s use in several data-driven techniques, however most deep learning techniques suffer from overfitting and stability issues. In this work, we propose an edge computing-based data-driven inversion technique based on supervised deep convolutional neural network to accurately reconstruct the subsurface velocities. Deep learning based data-driven technique depends mostly on bulk data training. In this work, we train our deep convolutional neural network (DCN) (UNet and InversionNet) on the raw seismic data and their corresponding velocity models during the training phase to learn the non-linear mapping between the seismic data and velocity models. The trained network is then used to estimate the velocity models from new input seismic data during the prediction phase. The prediction phase is performed on a resource-constrained edge device such as Raspberry Pi. Raspberry Pi provides real-time and on-device computational power to execute the inference process. In addition, we demonstrate robustness of our models to perform inversion in the presence on noise by performing both noise-aware and no-noise training and feeding the resulting trained models with noise at different signal-to-noise (SNR) ratio values. We make great efforts to achieve very feasible inference times on the Raspberry Pi for both models. Specifically, the inference times per prediction for UNet and InversionNet models on Raspberry Pi were 22 and 4 s respectively whilst inference times for both models on the GPU were 2 and 18 s which are very comparable. Finally, we have designed a user-friendly interactive graphical user interface (GUI) to automate the model execution and inversion process on the Raspberry Pi.

Manu, Daniel (ORCID:0000000154982677)↗

NCSU Flux Tower Data

NCSU Flux Tower Data Level b1: QC checks applied to measurements Data Format: CSV Description: See "instrument descripotion Site: Houston, TX; Tracking Aerosol Convection interactions ExpeRiment (HOU) Location: Houston, TX; AMF1 (main site for TRACER) Facility Code: M1 Category: Aerosol Properties Data Type: PI Data Source Instrument/Data: Sonic Anemometer, 3 Condensation Particle Counters, 1 SP2, 1 POPS Start Date: 2022-06-01 End Date: 2022-9-26 Contact PI: Markus Petters (mdpetter@ncsu.edu) Funding Source: DOE ASR award US Department of Energy, Office of Science, Biological and Environment Research (grant no. DE-SC 0021074) Instrument description The NCSU flux tower was located next to the AMF sampling pad. The flux tower consisted of a 10 m telescoping tower. Mounted at the top of the tower was a sonic anemometer (RM Young 8000) and a Krypton Hygrometer. A sample line (¼” conductive tubing) and communication line was laid to a trailer located underneath and slightly adjacent to the tower. The sample line brought aerosol inside the trailer at 4.5 L min-1, where it was distributed between 3 CPCs (TSI 3776c, Dc ~ 2.5 nm, TSI 3771, Dc ~10nm, and TSI 3772, Dc ~40 nm) with different size cuts. Also sampling was a printed particle optical spectrometer (POPS) and a single particle soot photometer (SP2). Please contact mdpetter@ncsu.edu for further information.

54 ENVIRONMENTAL SCIENCES↗

NCSU RDMA data

NCSU RDMA Data Level b1: QC checks applied to measurements Data Format: CSV Description: See "instrument description Site: Houston, TX; Tracking Aerosol Convection interactions ExpeRiment (HOU) Location: Houston, TX; AMF1 (main site for TRACER) Facility Code: M1 Category: Aerosol Properties Data Type: PI Data Source Instrument/Data: Nano-Scanning Mobility Particle (SMPS); A Radial Differential Mobility Analyzer (RDMA) coupled with 1 Condensation Particle Counter Start Date: 2022-06-01 End Date: 2022-9-26 Contact PI: Markus Petters (mdpetter@ncsu.edu) Funding Source: DOE ASR award US Department of Energy, Office of Science, Biological and Environment Research (grant no. DE-SC 0021074) Instrument description The NCSU RDMA was operated at a sheath-to-sample flow ratio of 5:1.5 L min−1. The RDMA was configured to scan from 5 to 55 nm. It was located into the temperature-controlled trailer adjacent to the NCSU Flux Tower to observe size distributions of the aerosols.The sample line was dried with three silica-gel driers in series, and then neutralized with X-ray neutralizer. Please contact mdpetter@ncsu.edu for further information.

54 ENVIRONMENTAL SCIENCES↗